New molecular probe can distinguish DNA and RNA sequences with unprecedented accuracy

In reliably identifying and binding to a target under a wide range of operating conditions, novel probe could be valuable tool in basic research and potentially in clinical diagnostics

Researchers at the Wyss Institute have developed a highly accurate molecular probe for identifying specific DNA and RNA sequences. This method could potentially improve the reliability of a variety of biotechnological and biomedical devices, such as microarray analysis, fluorescence in situ hybridization, and disease marker detection, which would provide powerful tools for basic research and for clinical diagnostics. The novel method is accurate enough to distinguish DNA sequences differing by as little as a single base, but also simple and robust enough for use across a broad range of temperatures, salinities, and concentrations.

The research was led by, David Zhang, Ph.D, a Postdoctoral Fellow at the Wyss Institute and in the Department of Systems Biology at Harvard Medical School, and Peng Yin, Ph.D., a core faculty member at the Wyss and an Assistant Professor in the Department of Systems Biology. Their findings appear in the online edition of Nature Chemistry. Zhang and Yin’s discovery is significant both as a scientific breakthrough and for its potential biotechnological and biomedical applications.

Many biotechnological and biomedical technologies and techniques depend on the specific binding between a target DNA (or RNA) sequence and a probe with a so-called “complementary sequence,” which is designed to optimally favor such binding. However, current probes often bind to incorrect sequences that are similar to–but not exactly the same as–the true target. It’s like baiting for salmon and catching trout instead–if there are many more trout in the river than salmon, you may catch a trout, even if you bait with the salmon’s favorite food. In the biotechnological and biomedical world, this type of unintended interaction can lead to a false positive, wherein benign DNA molecules could be mistaken for pathogen DNA. Zhang and Yin’s discovery greatly reduces the chance of incorrect binding. Their probe can reliably and specifically identify the true target: on average, it binds to a true target 26-fold more favorably than to an incorrect sequence that differs from the true target by just a single base. Importantly, once constructed, their probe can work in a wide range of experimental conditions. Such robustness can be critically important for real technological applications where the operational environment for the probe is difficult to predict or control.

The robust single-base specificity of the method will likely be a boon for a variety of applications: DNA of different pathogens, for example, can differ from each other by only a few bases. As another application, microRNAs are powerful regulatory molecules within the body, the over- or under-expression of which has been strongly linked to cancer and heart disease. MicroRNAs are also closely related in sequence, and distinguishing different microRNAs has important biomedical implications.

“This is a tremendously exciting step forward in basic scientific and engineering research, and we’re hopeful it will be developed into powerful technologies with significant applications.” said Wyss Institute Founding Director, Donald Ingber, M.D., Ph.D. Ingber is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Children’s Hospital Boston, and Professor of Bioengineering at Harvard’s School of Engineering and Applied Sciences.

The research was funded by the Wyss Institute and by grants from the National Institutes of Health, the National Science Foundation, and the Office of Naval Research.